Translational enhancer-element dependent vector systems

ABSTRACT

A translation enhancer-driven positive feedback vector system is disclosed which is designed to facilitate identification of a Translational Enhancer Element (TEE) and to provide a means for overexpression of gene products. The system exploits both transcriptional and translational approaches to control the expression levels of genes and/or gene products. Methods are also disclosed for screening libraries of random nucleotide sequences to identify translational elements and for overproduction of proteins, which have uses in both research and industrial environments.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. Ser. No. 11/509,293, filed Aug.23, 2006, which claims the benefit of priority under 35 U.S.C. §.119(e)of U.S. Ser. No. 60/711,149, filed Aug. 24, 2005, the entire contents ofwhich are incorporated herein by reference.

GRANT INFORMATION

This invention was made with support from NIH Grant No. GM 61725. Thegovernment has certain rights to this invention.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The contents of the text file named “PROO-007/D01US_SequenceListing_ST25.txt,” which was created on May 11, 2015 and is 20 KB insize, are hereby incorporated by reference in their entirety.

FIELD OF INVENTION

The present invention relates generally to vector constructs, and morespecifically to positive feedback vector constructs bearingtranslational enhancer elements (TEEs) in combination withtranscriptional elements and genes encoding transcription factors, wheresuch constructs may be used to identify other TEEs and to modulatelevels of protein expression.

BACKGROUND OF THE INVENTION

Eukaryotic mRNAs can initiate translation by either cap-dependent orcap-independent mechanisms. Presently, the relative contributions ofthese mechanisms to the proteome are unknown; however, some studiessuggest that cap-independent mechanisms may account for the translationof many mRNAs. For some mRNAs, cap-independent translation isfacilitated by sequence elements termed internal ribosome entry sites(IRESes). IRESes were first discovered in uncapped picornavirus RNAs andwere subsequently identified in other viral and cellular mRNAs frommammals, insects, and yeast. For some mRNAs, IRESes facilitatetranslation when cap-dependent initiation is less efficient or blocked.Internal initiation also facilitates the translation of particular mRNAswith 5′ leaders that are encumbered by numerous upstream AUGs or RNAsecondary structures.

A variety of evidence suggests that different IRESes vary in length,sequence composition, and in their requirements for initiation factorsor other trans-acting factors, suggesting that internal initiation oftranslation occurs by a number of different mechanisms. Some IRESes aremodular in composition. For example, an IRES module from the 5′ leaderof the Gtx homeodomain mRNA showed that maximal activity was obtainedwith sequences of 7 nucleotides. Various lines of evidence suggestedthat the mechanism underlying the activity of this sequence elementinvolves base pairing to a complementary sequence of 18S rRNA. Inanother study, a 22-nt IRES was identified in the 5′ leader of the Rbm3mRNA. In addition, it has been reported that the 5′ leader of thethymidine kinase mRNA contains an IRES-element and that the 5′ leader ofthe c-myc mRNA contains two short IRES elements.

The short size of some IRES/TEE modules suggests that they may beprevalent within mRNA populations.

Some IRES elements can also function as translation enhancer elements(TEEs), i.e., they can enhance translation in the context of amonocistronic mRNA. However, not all TEEs are IRESes and not all IRESesare TEEs.

SUMMARY OF THE INVENTION

The present invention describes a series of vectors designed to selectfor translational enhancer elements and overexpression of proteins ofinterest, and includes methods for the use of such vectors.

In one embodiment, a nucleic acid vector including a first constructthat includes two or more first transcriptional elements, a firstcistron encoding a transcription factor, and one or more firsttranslational enhancer elements (TEEs), where the transcription factoramplifies the transcription of at least one cistron of the firstconstruct is envisaged.

In a related aspect, the vector may include, but is not limited to, atleast one cistron on one or more second constructs including at leastone transcriptional unit. In a further related aspect, the firstconstruct and the at least one transcriptional unit of one or moresecond constructs include transcriptional elements that are targets forthe transcription factor encoded by the first cistron.

In a related aspect, such vectors may encode a gene product that is areporter protein, a therapeutic protein, an enzyme, an antigen, astructural protein, or an antibody.

In another aspect, at least one gene product blocks host proteinsynthesis. In a related aspect, the gene product may include, but is notlimited to, NSP3, L-proteinase, or proteinase 2A.

In one aspect, the vector includes at least one TEE that is resistant tothe activity of the product which blocks host protein synthesis, wherethe vector may contain transcriptional elements including, but notlimited to, minimal promoters, regulatable promoters, upstreamactivating sequences, and bacteriophage RNA polymerase specificpromoters.

In another embodiment, a nucleic acid vector including a first constructwhich includes a first transcriptional element, a first cistron encodinga first gene product, and a first translational enhancer element (TEE),wherein the TEE is resistant to an activity of a second gene productwhich blocks host protein synthesis is envisaged.

In a related aspect, TEEs include, HCV-IRES, IRESes, and IRES-elements,including, but not limited to, Gtx sequences (e.g., Gtx9-nt, Gtx8-nt,Gtx7-nt). In another related aspect, TEEs may include N-18 randomnucleotides which when operably linked to a cistron, increase the amountof protein induced per unit mRNA.

In one embodiment, a method of identifying a translational enhancerelement (TEE) is envisaged including inserting nucleotides from alibrary of nucleotides into a vector including a first construct whichincludes two or more first transcriptional elements, and a first cistronencoding a transcription factor, transfecting a cell with the vector,and determining the level of gene product translation from one or moresecond constructs in the transfected cell, where determining an enhancedlevel of translation of the gene product in the presence of the insertednucleotides is indicative of the presence of at least one TEE.

In a related aspect, the method may further include co-transfecting thecell with one or more second vectors, wherein the second vectors includethe one or more second constructs.

In another embodiment, a method of overexpressing a gene is envisagedincluding, transfecting a cell with a vector including a first constructincluding two or more first transcriptional elements, a first cistronencoding a transcription factor, and one or more first translationenhancer elements (TEEs), and expressing a gene product from one or moresecond constructs including a second TEE, where the resulting level ofgene product expressed from the second construct is enhanced in thepresence of the first and second TEEs.

In a related aspect, the method may further include co-transfecting thecell with one or more second vectors including the one or more secondconstructs. In a further related aspect, the method may further includeexpressing a gene from a third construct including a third TEE, wherethe gene from the third construct encodes one or more gene productswhich block host protein synthesis. In a related aspect, the method mayfurther include co-transfecting the cell with a third vector includingthe third construct.

In one embodiment, a method of overexpressing a gene is envisagedincluding transfecting a cell with a vector including a first constructincluding at least one first transcriptional element, a first cistronencoding a first gene product, and at least one translational enhancerelement (TEE) and expressing a gene from one or more second constructsencoding a protein which blocks host protein synthesis, where theresulting level of gene product expressed from the first construct isenhanced in the presence of the blocking protein.

Exemplary methods and compositions according to this invention, aredescribed in greater detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a translation enhancer-driven positive feedbackvector. A schematic representation of the positive feedback vector isshown along with the various promoter (P1) and transcriptional enhancer(P2) sequences, transcription factor (TF) genes, and a protein ofinterest. The transcription factor gene and the gene of interest may beon the same plasmid or on different plasmids. For the selectionapplication, a random nucleotide sequence (N), n nucleotides in lengthis present in the 5′ leader of the transcription factor mRNA. A sequencethat functions as a translational enhancer element (TEE) will facilitatethe translation of this mRNA. The encoded transcription factor will thenbind to sites in the promoters of the two genes and increase theirtranscription.

FIG. 2 illustrates a translation enhancer-driven positive feedbackvector with a third protein to block host protein synthesis. The firsttwo genes (transcription factor gene and gene of interest) are the sameas in FIG. 1 except that all three mRNAs contain a TEE in their 5′leader. The third protein (e.g., the Rotavirus NSP3 protein) willincrease the translation of the first two encoded mRNAs by blocking thetranslation of host mRNAs and reducing the competition from them. Thethird gene is under the transcriptional control of promoter P3, which iseither a constitutive promoter or an inducible promoter. P3 may alsoinclude promoter elements P1 and P2. For the selection application, themRNAs for the gene of interest and third protein will contain a knownTEE, while the transcription factor gene will contain a randomnucleotide sequence. In this scenario, the TEE is resistant to theactivity of the third protein. For a protein production application, allthree genes may contain a known TEE that is resistant to the activity ofthe third protein. The three genes may be on one, two, or threedifferent plasmids.

FIG. 3 illustrates a protein overexpression vector. The first geneencodes the gene of interest. As shown in FIG. 2, each gene contains aTEE in its 5′ leader. In this scenario, the TEE is resistant to theactivity of the other encoded protein (e.g., NSP3). The two genes may beon one or two different plasmids.

FIG. 4 shows a restriction map for a positive feedback reporting vector(SEQ ID NO: 1). Sequences in bold represent: 1) promoter sequences,including TATA boxes and upstream activating sequences (UAS); 2)GAL4R1-GAL4R4, primer sequences for PCR amplification; 3) ATG and TAA,start and stop translation sequences, respectively; and 4) HRGB1-HRGB4,primer sequences for PCR amplification.

FIG. 5 shows one-cut enzymes for pUAS-GV16-UAS-EGFP (SEQ ID NO: 1).

DETAILED DESCRIPTION OF THE INVENTION

Before the present compositions and methods are described, it isunderstood that this invention is not limited to the particularmethodology, protocols, and reagents described as these may vary. It isalso to be understood that the terminology used herein is for thepurpose of describing particular embodiments only, and is not intendedto limit the scope of the present invention which will be described bythe appended claims.

It must be noted that as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural reference unless thecontext clearly dictates otherwise. Thus, for example, reference to “acell” includes a plurality of such cells, reference to “a protein”includes one or more proteins and equivalents thereof known to thoseskilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meanings as commonly understood by one of ordinary skillin the art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, the methods, devices,and materials are now described. All publications mentioned herein areincorporated herein by reference for the purpose of describing anddisclosing the proteins, nucleic acids, and methodologies which arereported in the publications which might be used in connection with theinvention. Nothing herein is to be construed as an admission that theinvention is not entitled to antedate such disclosure by virtue of priorinvention.

As used herein, “translational enhancer element (TEE),” includinggrammatical variations thereof, means cis-acting sequences that increasethe amount of protein induced per unit mRNA. In a related aspect, TEEsinclude, HCV-IRES, IRESes, and IRES-elements, including, but not limitedto, Gtx sequences (e.g., Gtx9-nt, Gtx8-nt, Gtx7-nt). In another relatedaspect, TEEs may include N-18 random nucleotides which when operablylinked to a cistron, increase the amount of protein induced per unitmRNA.

In a further related aspect, sequences for such elements include, butare not limited to, GenBank accession numbers AX205123 and AX205116 (GtxIRES element), D17763 (HCV-IRES, 5′-untranslated region).

As used herein, “cistron” including grammatical variations thereof,means a unit of DNA that codes for a single polypeptide or protein.

As used herein, “transcriptional unit,” including grammatical variationsthereof, means the segment of DNA within which the synthesis of RNAoccurs.

As used herein, “nucleotide sequence,” “nucleic acid sequence,” “nucleicacid,” or “polynucleotide,” refers to a deoxyribonucleotide orribonucleotide polymer in either single- or double-stranded form, andunless otherwise limited, encompasses known analogs of naturalnucleotides that hybridize to nucleic acids in a manner similar tonaturally-occurring nucleotides. Nucleic acid sequences can be, e.g.,prokaryotic sequences, eukaryotic mRNA sequences, cDNA sequences fromeukaryotic mRNA, genomic DNA sequences from eukaryotic DNA (e.g.,mammalian DNA), and synthetic DNA or RNA sequences, but are not limitedthereto.

In a related aspect, synthetic methods for preparing a nucleotidesequence include, for example, the phosphotriester and phosphodiestermethods (see Narang et al., Meth. Enzymol. 68:90, (1979); U.S. Pat. No.4,356,270, U.S. Pat. No. 4,458,066, U.S. Pat. No. 4,416,988, U.S. Pat.No. 4,293,652; and Brown et al., Meth Enzymol 68:109, (1979), each ofwhich is incorporated herein by reference).

As used herein, “promoter” including grammatical variations thereof,means a nucleic acid sequence capable of directing transcription. Avariety of promoter sequences are known in the art. For example, suchelements can include, but are not limited to, TATA-boxes, CCAAT-boxes,bacteriophage RNA polymerase specific promoters (T7: TAATACGACTCACTATAGG(SEQ ID NO: 4); SP6: ATTTAGGTGACACTATAGA (SEQ ID NO: 5); and T3:AATTAACCCTCACTAAAGG (SEQ ID NO: 6)), an SP1 site (GGGCGG), and a cyclicAMP response element (TGACGTCA).

As used herein, “transcriptional element,” including grammaticalvariations thereof, means a cis-acting site on DNA that allows forinitiation or stimulation of initiation of transcription, usuallythrough recognition by a transcription factor. For example, suchelements exist in motifs including, but not limited to, CACGTG (c-Myc),TGAc/gTc/aA (c-Fos), and t/aGATA (GATA). In a related aspect, the vectormay contain one or more transcriptional elements comprising one or moreupstream activating sequences (UAS), including but not limited to, theconsensus GAGTACTGTCCTCCGAGCG (SEQ ID NO: 7).

As used herein, “transcription factor,” including grammatical variationsthereof, means any protein required to initiate or regulatetranscription. For example, such factors include, but are not limitedto, c-Myc, c-Fos, c-Jun, CREB, cEts, GATA, GAL4, GAL4/Vp16, c-Myb, MyoD,NF-.kappa.B, bacteriophage-specific RNA polymerases, Hif-1, and TRE.

In a further related aspect, sequences for such factors include, but arenot limited to, GenBank accession numbers K02276 (c-Myc), K00650(c-fos), BC002981 (c-jun), M27691 (CREB), X14798 (cEts), M77810 (GATA),K01486 (GAL4), AY136632 (GAL4/Vp16), M95584 (c-Myb), M84918 (MyoD),2006293A (NF-.kappa.B), NP 853568 (SP6 RNA polymerase), AAB28111 (T7 RNApolymerase), NP 523301 (T3 RNA polymerase), AF364604 (HIF-1), and X63547(TRE).

As used herein, “transcriptional activator regions,” includinggrammatical variations thereof, means protein sequences that, whentethered to DNA near a promoter, activate transcription by contactingtargets in the transcriptional machinery (see, e.g., Xiangyang et al.,Proc Natl Acad Sci USA (2000) 97:1988-1992). Activator regions,characterized by having an excess of acidic amino acid residues, arefound in a wide array of eukaryotic activators, including the yeastactivators Gal4, GCN4, and the herpesvirus activator VP16.

As used herein, “construct,” including grammatical variations thereof,means nucleic acid sequence elements arranged in a definite pattern oforganization such that the expression of genes/gene products that areoperably linked to these elements can be predictably controlled. In arelated aspect, a wide variety of heterologous sequences may be includedin the construct, including, but not limited to, for example, sequenceswhich encode growth factors, cytokines, chemokines, lymphokines, toxins,prodrugs, antibodies, antigens, ribozymes, as well as antisensesequences. In another related aspect, such heterologous sequences encodeproteins which can serve as therapeutic modalities.

As used herein, “vector,” including grammatical variations thereof,means the DNA of any transmissible agent (e.g., plasmid or virus) intowhich a segment of foreign DNA can be spliced in order to introduce theforeign DNA into host cells to promote its replication and/ortranscription.

As disclosed herein, a vector comprising a construct is useful foridentifying translational enhancer elements. In one embodiment, theconstruct is contained in a vector, which generally is an expressionvector that contains certain components, but otherwise can vary widelyin sequence and in functional element content. The vector also cancontain sequences that facilitate recombinant DNA manipulations,including, for example, elements that allow propagation of the vector ina particular host cell (e.g., a bacterial cell, insect cell, yeast cell,or mammalian cell), selection of cells containing the vector (e.g.,antibiotic resistance genes for selection in bacterial or mammaliancells), and cloning sites for introduction of reporter genes or theelements to be examined (e.g., restriction endonuclease sites orrecombinase recognition sites).

Preferably, constructs as envisaged provide the advantage that theactivity of an oligonucleotide can be examined in the context or milieuof the whole eukaryotic chromosome. A chromosome offers unique andcomplex regulatory features with respect to the control of geneexpression, including translation. As such, it is advantageous to have asystem and method for obtaining regulatory oligonucleotides thatfunction in the context of a chromosome. Thus, a method of the inventioncan be practiced such that integration of the expression vector into theeukaryotic host cell chromosome occurs, forming a stable construct priorto selection for an expressed reporter molecule.

A vector comprising a construct as envisaged can be integrated into achromosome by a variety of methods and under a variety of conditions.Thus, the present invention should not be construed as limited to theexemplified methods. Shotgun transfection, for example, can result instable integration if selection pressure is maintained upon thetransfected cell through several generations of cell division, duringwhich time the transfected nucleic acid construct becomes stablyintegrated into the cell genome. Directional vectors, which canintegrate into a host cell chromosome and form a stable integrant, alsocan be used. These vectors can be based on targeted homologousrecombination, which restricts the site of integration to regions of thechromosome having the homology, and can be based on viral vectors, whichcan randomly associate with the chromosome and form a stable integrant,or can utilize site specific recombination methods and reagents such asa lox-Cre system and the like.

Shotgun transfections can be accomplished by a variety of well knownmethods, including, for example, electroporation, calcium phosphatemediated transfection, DEAE dextran mediated transfection, a biolisticmethod, a lipofectin method, and the like. For random shotguntransfections, the culture conditions are maintained for severalgenerations of cell division to ensure that a stable integration hasresulted and, generally, a selective pressure also is applied. A viralvector based integration method also can be used and provides theadvantage that the method is more rapid and establishes a stableintegration by the first generation of cell division. A viral vectorbased integration also provides the advantage that the transfection(infection) can be performed at a low vector:cell ratio, which increasesthe probability of single copy transfection of the cell. A single copyexpression vector in the cell during selection increases the reliabilitythat an observed regulatory activity is due to a particularoligonucleotide, and facilitates isolation of such an oligonucleotides.

Reference is made herein to techniques commonly known in the art.Guidance in the application of such techniques can be found, e.g., inAusubel et al. eds., 1995, Current Protocols In Molecular Biology, andin Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory Press, NY, the contents of which areincorporated herein by reference.

Previous studies have generated synthetic IRESes containing multipleindividual IRES elements and showed that this multimerization led tohigher, and in some cases exponential, increases in IRES activity. Tofacilitate the discovery process, a number of methods to screen for IRESelements in mammalian cells and in yeast have been developed. In all ofthese methods, dicistronic mRNAs containing a library of randomnucleotide sequences in the intercistronic sequences (ICS) wereexpressed in cells, and those cells containing IRES elements wereidentified on the basis of the expression of the second cistron. Themammalian methods used a fluorescent reporter protein as the secondcistron, and positive cells were identified with FACS. However, alimitation of these methods was that the activities of individual IRESelements were relatively low, leading to a large number of falsepositive cells.

To circumvent this signal-to-noise problem, the present inventiondescribes a positive feedback based system where one cistron encoding aTEE containing transcription factor triggers a positive feedback loop inwhich the transcription factor binds to a select sequence in theupstream promoter of the cistron encoding the factor and one or morecistrons encoding an mRNA of interest, thereby increasing thetranscription of both mRNAs. More mRNA results in more transcriptionfactor, leading to ever-increasing amounts of both the transcriptionfactor and protein of interest mRNA and the encoded proteins.

In one embodiment, the vector system is a translation enhancer-drivenpositive feedback vector (e.g., see FIG. 1). In one aspect, a constructexpresses two mRNAs: one encoding a protein of interest which may be areporter protein and the other encoding a transcription factor. Thetranscription of both mRNAs is driven by minimal promoters but can beenhanced by the expression of the transcription factor via binding sitesfor the transcription factor that are located in the promoters of bothgenes. A small amount of transcription factor mRNA is expressed from theminimal promoter but the translation of this mRNA is blocked by anobstacle in the 5′ leader of the mRNA encoding the transcription factor.This obstacle may be a stable stem-loop structure and/or upstream AUGinitiation codons. The synthesis of this transcription factor isdependent on the presence of a translation enhancer in the mRNA encodingthis factor.

The translational enhancer can be located in the 5′ leader of the mRNA,downstream of the inhibitory elements but upstream of the initiationcodon, or it may be located in the 3′ untranslated region (UTR). In oneaspect, the TEE is situated in the 5′ leader sequence which is containedwithin a cistron.

Utilization of this vector system may require that the encodedtranscription factor not be expressed in the cells of interest. Forexample, a transcription factor (e.g., Gal4/Vp16), that contains the DNAbinding domain of the yeast GAL4 transcription factor is suitable foruse in mammalian cells because mammalian genes do not appear to betargets of this transcription factor. Other suitable transcriptionfactors include, but are not limited to, those that are expressedendogenously at very low levels, or are absent in the cells of interest.For example, bacteriophage specific-RNA polymerases (e.g., T7, T3, andSP6 RNA polymerases) are suitable for use in both mammalian cells andyeast. The genes as envisaged can be encoded by one or more vectors.

In one embodiment, the vector system can be used to identify a TEE. Anoligonucleotide to be examined for translational activity can beoperatively linked to an expressible polynucleotide, which, for example,can encode a reporter molecule. As used herein, the term “operativelylinked” means that a regulatory element, which can be a syntheticregulatory oligonucleotide or an oligonucleotide to be examined for suchactivity, is positioned with respect to a translatable nucleotidesequence such that the regulatory element can affect its regulatoryactivity. An oligonucleotide having translational enhancer activitygenerally is positioned within about 1 to 500 nucleotides, particularlywithin about 1 to 100 nucleotides of a translation start site.

A library of randomized oligonucleotides to be examined fortranslational regulatory activity can be provided, and one or moreindividual members of the library can be cloned into multiple copies ofthe construct of the vector. The oligonucleotide to be examined fortranslational regulatory activity is introduced such that it isoperatively linked to the minimal promoter element in the construct and,therefore, has the potential to function as a TEE. In this way, alibrary of different constructs, which can be contained in a vector, isformed, each construct differing in the introduced potential regulatoryoligonucleotide sequence.

Oligonucleotides to be examined for translational regulatory activitycan be, for example, cDNA sequences encoding 5′ UTRs of cellular mRNAs,including a library of such cDNA molecules. Furthermore, as disclosedherein, TEEs identified according to a method of the invention,including synthetic TEE elements, have been found to be complementary tooligonucleotide sequences of ribosomal RNA, particularly to un-basepaired oligonucleotide sequences of rRNA, which are interspersed amongdouble stranded regions that form due to hybridization of selfcomplementary sequences within rRNA. Accordingly, oligonucleotides to beexamined for translational regulatory activity, can be designed based ontheir being complementary to an oligonucleotide sequence of rRNA,particularly to an un-base paired oligonucleotide sequence of rRNA suchas a yeast, mouse or human rRNA (e.g., see GenBank Accession Nos.V01335, X00686, X03205, each of which is incorporated herein byreference). In addition, oligonucleotides to be examined fortranslational regulatory activity can be a library of variegatedoligonucleotide sequences (see, for example, U.S. Pat. No. 5,837,500,incorporated herein by reference), which can be based, for example, on atranslational enhancer element as disclosed herein or identified using amethod of the invention, or on an oligonucleotide sequence complementaryto an un-base paired region of a rRNA.

The oligonucleotides identified herein as having translationalregulatory activity provide modules that can be used alone or combinedwith each other to produce desired activities. For example, concatemersof an identified TEE can vastly increase polypeptide expression from anassociated cistron, including concatemers of 2, 5, 10, 20, 35, 50 or 75copies of a TEE, which independently can be multiple copies of the sameor different TEEs, and which can be operatively linked adjacent to eachother or separated by spacer nucleotide sequences that can vary from 1to about 100 nucleotides in length.

A synthetic translational regulatory element can be identified byscreening, for example, a library of oligonucleotides containing a largenumber of different nucleotide sequences. The oligonucleotides can bevariegated oligonucleotide sequences, which are based on but differentfrom a known translational regulatory element, for example, anoligonucleotide complementary to an un-base paired sequence of a rRNA,or can be a random oligonucleotide library. The use of randomizedoligonucleotides (e.g., N18) provides the advantage that no priorknowledge is required of the nucleotide sequence, and provides theadditional advantage that completely new regulatory elements can beidentified. Methods for making a combinatorial library of nucleotidesequences or a variegated population of nucleotide sequences are wellknown in the art (see, for example, U.S. Pat. No. 5,837,500; U.S. Pat.No. 5,622,699; U.S. Pat. No. 5,206,347; Scott and Smith, Science249:386-390, 1992; Markland et al., Gene 109:13 19, 1991; O'Connell etal., Proc Natl Acad Sci, USA 93:5883-5887, 1996; Tuerk and Gold, Science249:505-510, 1990; Gold et al., Ann Rev Biochem 64:763-797, 1995; eachof which is incorporated herein by reference).

A synthetic TEE oligonucleotide, which can be obtained using a method ofthe invention, can increase or decrease the level of translation of anmRNA containing the oligonucleotide. In particular, a TEEoligonucleotide can selectively regulate translation in a contextspecific manner, depending, for example, on the cell type forexpression, the nature of the TEE sequence, or the presence of othereffector sequences in the construct.

A regulatory element can be of various lengths from a few nucleotides toseveral hundred nucleotides. Thus, the length of an oligonucleotide in alibrary of oligonucleotides to be screened can be any length, includingoligonucleotides as short as about 6 nucleotides or as long as about 100nucleotides or more. Generally, the oligonucleotides to be examined areabout 6, 12, 18, 30 nucleotides or the like in length. The complexity ofthe library, i.e., the number of unique members, also can vary, althoughpreferably the library has a high complexity so as to increase thelikelihood that regulatory sequences are present. Libraries can be madeusing any method known in the art, including, for example, using anoligonucleotide synthesizer and standard oligonucleotide syntheticchemistry. Where the oligonucleotides are to be incorporated into avector, the library complexity depends in part on the size of theexpression vector population being used to clone the random library andtransfect cells. Thus, a theoretical limitation for the complexity ofthe library also relates to utilization of the library content by therecipient expression vector and by the transfected cells, as well as bythe complexity that can be obtained using a particular method ofoligonucleotide synthesis.

To identify TEEs, libraries of constructs that contain either randomnucleotide sequences or cDNA segments of 5′ leaders of mRNAs areintroduced into cells. Cells containing a construct with a TEE upstreamof the transcription factor will trigger the positive feedback mechanismand produce large amounts of both proteins. If one of the proteins is areporter protein, its activity can be readily assayed. For example, ifthe reporter is enhanced green fluorescent protein (EGFP), fluorescenceactivated cell sorting (FACS) can be used to identify cells expressingthe fluorescent protein. In a preferred embodiment of the presentinvention, the means of detecting the presence of GFP in transfectedcells is by fluorescence microscopy and by FACS. However, it will bereadily understood by those of skill in the art that other means fordetecting the presence of GFP may also be used in the practice of thepresent invention. The means of detecting GFP or of tracking ormonitoring cells which have been transfected with a construct of thepresent invention may be any means whereby the presence GFP protein isdetectable. For example, optical imaging, infrared imaging of geneexpression, and flow cytometry may also be used.

In a related aspect, other reporter proteins can include, but are notlimited to, enhanced yellow fluorescent protein (EYFP), enhanced cyanfluorescent protein (ECFP), luciferase, .beta.-galactosidase,.beta.-glucuronidase, alkaline phosphatase, and chloramphenicolacetyltransferase.

In a related aspect, such a vector can be used to identify sequencesthat enhance translation by various mechanisms, including but notlimited to, cap-independent and cap-dependent mechanisms.

In one aspect, the vector system as envisaged can be used to overexpressanother protein of interest. In a related aspect, the mRNA encoding thetranscription factor will contain a known TEE. Such a system may besuitable for the batch production of proteins, where the transcriptionfactor is under the control of a regulatable promoter, so that cells canbe grown to a large volume before the positive feedback mechanisms andlarge scale protein production are induced by, for example, an inducingagent.

The term “inducing agent” is used to refer to a chemical, biological orphysical agent that effects translation from an inducible translationalregulatory element. In response to exposure to an inducing agent,translation from the element generally is initiated de novo or isincreased above a basal or constitutive level of expression. Suchinduction can be identified using the methods disclosed herein,including detecting an increased level of a reporter polypeptide encodedby the expressible polynucleotide that is operatively linked to the TEE.An inducing agent can be, for example, a stress condition to which acell is exposed, for example, a heat or cold shock, a toxic agent suchas a heavy metal ion, or a lack of a nutrient, hormone, growth factor,or the like; or can be exposure to a molecule that affects the growth ordifferentiation state of a cell such as a hormone or a growth factor. Asdisclosed herein, the translational regulatory activity of anoligonucleotide can be examined in cells that are exposed to particularconditions or agents, or in cells of a particular cell type, andoligonucleotides that have translational regulatory activity in responseto and only under the specified conditions or in a specific cell typecan be identified.

In another embodiment, a vector system is envisaged which expresses athird mRNA that encodes a protein that can increase the translation ofthe other two encoded mRNAs by decreasing the translation of cellularmRNAs (FIG. 2). In one aspect, the expression of the third proteindecreases competition from the cellular mRNAs and leads to an increasedsignal-to-noise ratio in the selection application.

In a related aspect, the third protein may be a viral protein thatblocks translation of host mRNAs and thereby decreases the competitionarising from these mRNAs. Viral proteins include, but are not limitedto, NSP3, L-proteinase, or proteinase 2A. For example, without beingbound to theory, the NSP3 protein blocks cap-dependent translation bybinding to the eukaryotic initiation factor 4G (eIF4G) with highaffinity, displacing the poly(A) binding protein, disrupting mRNAcirculation, and dramatically decreasing efficiency. In this scenario,the three vector encoded mRNAs contain features that prevent theirtranslation from being blocked. For example, where a TEE does notrequire eIF4G for activity, such an element would be resistant to NSP3(e.g., Gtx IRES elements and the Cricket paralysis virus IRES). In arelated aspect, the third protein can be under the control of theencoded transcription factor or under the control of an induciblepromoter.

In one embodiment, the vector system expresses a gene product or proteinof interest and a third protein, where the third protein blocks hostprotein synthesis (FIG. 3). In a related aspect, the gene product orprotein of interest will contain features that prevent their translationfrom being blocked. In another related aspect, the genes are transcribedby either a constitutive promoter or an inducible promoter.

A kit of the invention is also envisaged. Such a kit can contain apackaging material, for example, a container having a TEE containingoligonucleotide according to the invention and a label that indicatesuses of the oligonucleotide for regulating translation of apolynucleotide in an expression vector or other expression construct. Inone embodiment, the system, preferably in kit form, provides anintegrating expression vector for use in selecting a TEE oligonucleotideusing a method as disclosed herein. Such a kit can contain a packagingmaterial, which comprises a container having an integrating expressionvector and a label that indicates uses of the vector for selectingoligonucleotide sequences capable of regulatory function.

Instructions for use of the packaged components also can be included ina kit of the invention. Such instructions for use generally include atangible expression describing the components, for example, a TEEcontaining oligonucleotide, including its concentration and sequencecharacteristics, and can include a method parameter such as the mannerby which the reagent can by utilized for its intended purpose. Thereagents, including the oligonucleotide, which can be contained in avector or operably linked to an expressible polynucleotide, can beprovided in solution, as a liquid dispersion, or as a substantially drypowder, for example, in a lyophilized form. The packaging materials canbe any materials customarily utilized in kits or systems, for example,materials that facilitate manipulation of the regulatoryoligonucleotides and, if present, of the vector, which can be anexpression vector. The package can be any type of package, including asolid matrix or material such as glass, plastic (e.g., polyethylene,polypropylene, and polycarbonate), paper, foil, or the like, which canhold within fixed limits a reagent such as a TEE containingoligonucleotide or vector. Thus, for example, a package can be a bottle,vial, plastic and plastic-foil laminated envelope, or the like containerused to contain a contemplated reagent. The package also can compriseone or more containers for holding different components of the kit.

The following examples are intended to illustrate but not limit theinvention.

EXAMPLES Example 1 Experimental Procedures/Materials

Construction of Vectors

The constructs used in the present invention express one or morecistronic mRNAs that encode a transcription factor, protein of interestand/or a protein blocking host protein synthesis. Promoters used todrive transcription of the cistronic mRNAs consist of a minimal promoter(TATA box) or regulatable promoter, alone or in combination with one ormore other transcriptional elements, including upstream activatingsequences (UAS) and bacteriophage specific promoters. For feedbackvectors, a first cistron would comprise a gene encoding a transcriptionfactor, which is inserted downstream from a known or unknown TEE. Onesuch construct, containing a known TEE, would comprise a TATA boxpromoter element, one or more UAS sequences, and one or more Gtx modulesupstream from a cistron encoding Gal4/Vp16.

Example 2 Positive Feedback Reporter Vector for Identifying TEE Elements

Construction

As shown in FIG. 4, the promoters used to drive transcription in thisexample comprise a minimal promoter (TATA box) in combination with fourcopies of the GAL4 upstream activating sequence (UAS). The firsttranscription unit encodes the GAL4/VP16 fusion protein and the secondtranscription unit encodes EGFP. The TEE insertion site (denoted by “N”in FIG. 4) contains nucleotides from a library of 18 random nucleotides.The vector backbone is based on plasmid pHRG-B (Promega, Madison, Wis.).The original BamHI site in pHRG-B was mutated so that both EcoRI andBamHI sites in the TEE insertion site were unique. The random N.sub.18fragments are cloned into this reporter vector by using the EcoRI andBamHI restriction sites.

Cell Culture and Transfection Analysis

Reporter constructs are transfected into Chinese hamster ovary cells(CHO) (2.times.10.sup.4) by using FuGENE 6™ (Roche, Alameda, Calif.).Transfection efficiencies are normalized by co-transfection with a LacZreporter gene construct (pCMV.beta., Clontech, Mountainview, Calif.).Cells are harvested 3 days after transfection and sorted by FACS on aFACSVantage SE™ (Becton Dickinson, Franklin Lakes, N.J.) (Also, seeOwens et al., Proc Natl Acad Sci USA (2004) 101:9590-9594)..beta.-galactosidase assays may be performed by methods known in theart. For example, see Chappell et al., Proc Natl Acad Sci USA (2000)97:1536-1541.

Double-stranded oligonucleotides containing N18 sequences are clonedinto the TEE assay site of the positive feedback vector by using EcoRIand BamHI restriction sites. Overnight ligations are performed using T4DNA ligase at 16.degree. C. The resulting ligation mix is transfectedinto CHO cells, and FACS analysis is performed as above. For each FACSanalysis, the first 100,000 cells are analyzed and a sorting window isdrawn to select the cells with the highest EGFP expression. DNA isextracted from cells recovered by FACS and PCR reactions are carried-outby using primers to sequences that flank the EcoRI and BamHI restrictionsites. After digestion with both EcoRI and BamHI restriction enzymes,the resulting fragments are re-cloned into the same amplification vectorand retested.

For determining the number of plasmids per transfected cell, equalamounts of two plasmids are mixed, CMV-EGFP and CMV-enhanced cyanfluorescent protein (CMV-ECFP; Clontech, Mountainview, Calif.). Thecloning vector pBluescript-KS II™ (Stratagene, La Jolla, Calif.) is usedas filler for co-transfection. CHO cells are transfected with thedifferent mixtures and FACS analysis is performed 2 days later to assessthe expression of both EGFP and ECFP.

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of illustrative embodiments, it will be apparentto those of skill in the art that variations may be applied to thecomposition, methods and in the steps or in the sequence of steps of themethods described herein without departing from the concept, spirit, andscope of the invention. More specifically, it will be apparent thatcertain agents which are both chemically and physiologically related maybe substituted for the agents described herein while the same or similarresults would be achieved. Although the invention has been describedwith reference to the above examples, it will be understood thatmodifications and variations are encompassed within the spirit and scopeof the invention.

1.-25. (canceled)
 26. A method of identifying a translational enhancerelement (TEE) comprising: a) inserting nucleotides from a library ofnucleotides into a vector comprising a first construct comprising two ormore first transcriptional elements, and a first cistron encoding atranscription factor; b) transfecting a cell with the vector of step(a); and c) determining the level of gene product translation from oneor more second constructs in the cell of step (b), wherein determiningan enhanced level of translation of the gene product in the presence ofthe inserted nucleotides is indicative of the presence of at least oneTEE.
 27. The method of claim 26, further comprising co-transfecting thecell of step (b) with one or more second vectors comprising the one ormore second constructs.
 28. The method of claim 26, wherein at least oneof the sequences comprising the first transcriptional elements is notthe target of transcription factors endogenous to the cell.
 29. Themethod of claim 26, wherein the transcription factor is not endogenousto the cell.
 30. The method of claim 26, wherein two or more secondconstructs comprise at least one transcriptional element and a TEE whichare 5′-proximal to at least one cistron contained therein.
 31. Themethod of claim 30, wherein one of the second constructs comprises acistron encoding a gene product which blocks host protein synthesis. 32.The method of claim 31, wherein the blocking gene product is NSP3,L-proteinase, or proteinase 2A.
 33. The method of claim 31, wherein theat least one TEE is an IRES, HCV-IRES or IRES element.
 34. The method ofclaim 33, wherein the IRES, HCV-IRES or IRES element is a Gtx sequence.35. The method of claim 33, wherein at least one TEE is resistant to theactivity of the product which blocks host protein synthesis.
 36. Themethod of claim 26, wherein the two or more transcriptional elements areselected from the group consisting of minimal promoters, regulatablepromoters, upstream activating sequences, and bacteriophage RNApolymerase specific promoters.
 37. The method of claim 26, wherein thefirst cistron encodes GAL4/VP16, GAL4, or a bacteriophage specific RNApolymerase.
 38. A method of overexpressing a gene comprising: a)transfecting a cell with a vector comprising a first constructcomprising two or more first transcriptional elements, a first cistronencoding a transcription factor, and one or more first translationenhancer elements (TEEs); and b) expressing, in the cell of step (a), agene product from one or more second constructs comprising a second TEE,wherein the resulting level of gene product expressed from the secondconstruct is enhanced in the presence of the first and second TEEs. 39.The method of claim 38, further comprising co-transfecting the cell ofstep (a) with one or more second vectors comprising the one or moresecond constructs.
 40. The method of claim 38, further comprisingexpressing, in the cell of step (a), a gene from a third constructcomprising a third TEE, wherein the gene from the third constructencodes one or more gene products which block host protein synthesis.41. The method of claim 40, further comprising co-transfecting the cellof step (a) with a third vector comprising the third construct.
 42. Themethod of claim 40, wherein the blocking gene product is NSP3,L-proteinase, or proteinase 2A.
 43. The method of claim 38, wherein thetwo or more transcriptional elements are selected from the groupconsisting of minimal promoters, regulatable promoters, upstreamactivating sequences, and bacteriophage RNA polymerase specificpromoters.
 44. The method of claim 38, wherein the first cistron encodesGAL4/VP16, GAL4, or a bacteriophage specific RNA polymerase.
 45. Themethod of claim 33, wherein the at least one TEE is an IRES, HCV-IRES orIRES element.
 46. The method of claim 45, wherein the IRES, HCV-IRES orIRES element is a Gtx sequence.
 47. The method of claim 33, wherein theat least one TEE is an N18 sequence, wherein N18 is a randomoligonucleotide.
 48. A method of overexpressing a gene comprising: a)transfecting a cell with a vector comprising a first constructcomprising at least one first transcriptional element, a first cistronencoding a first gene product, and at least one translational enhancerelement (TEE); and b) expressing, in the cell of step (a), a gene fromone or more second constructs encoding a protein which blocks hostprotein synthesis with one or more TEEs, wherein the resulting level ofgene product expressed from the first construct is enhanced in thepresence of the blocking protein.
 49. The method of claim 48, furthercomprising co-transfecting the cell of step (a) with a second vectorcomprising the one or more second constructs.
 50. The method of claim48, wherein the TEE is resistant to the blocking protein.
 51. The methodof claim 48, wherein the two or more transcriptional elements areselected from the group consisting of minimal promoters and regulatablepromoters.
 52. The method of claim 48, wherein the at least one TEE isan IRES, HCV-IRES or IRES element.
 53. The method of claim 52, whereinthe IRES, HCV-IRES or IRES element is a Gtx sequence.
 54. The method ofclaim 48, wherein the at least one TEE is an N18 sequence, wherein N18is a random oligonucleotide.
 55. The method of claim 48, wherein theblocking gene product is NSP3, L-proteinase, or proteinase 2A.